On 2/14/15, Matt Mahoney via AGI <[email protected]> wrote: > The paper doesn't claim a polynomial time solution to the Hamiltonian > path problem. What they did was solve one particular problem with 3 > nodes using bacterial DNA. The problem was to find a path from A to C > given directed edges {A->B, B->C, A->C} that goes through all 3 nodes > exactly once. The bacteria computed the solution is A->B->C. The > authors note that the number of bacteria that would be needed to solve > a problem with n nodes would grow as O(n!). It is only polynomial time > in the sense that the population will grow exponentially, given enough > food. > > The algorithm is to assign a DNA sequence for each node A, B, C, and > to create DNA strings AB, BC, AC and their complements and let them > combine with the constraint that the string starts with A and ends > with C. One possible combination is AC by itself. Another is AB-BC. A > solution will express the proteins A, B, and C exactly once each. A > computation has to be able to test this. In the experiment, two of the > proteins, A and B, fluoresce red and green respectively. If both are > present, then the colony will glow yellow. To read the output, they > collect the yellow bacteria and sequence its DNA. > > There is an additional complication that you need to insert a sequence > into the middle of each protein that attracts an enzyme that cuts DNA, > without destroying the function of the protein. The authors did this. > You also need to encode a ribosome attracting promoter sequence ahead > of the first node and a stop codon after the last. All of this has to > be done in such a way that all possible sequences in the search space > still result in viable organisms. > > Anyway, good luck using this approach to solving 3-SAT. >
The main problem here -- what happens if you drop ur program! Everybody dies of salmonella or e-coli. I'm not trying to throw a damper on this idea. > > On Sat, Feb 14, 2015 at 12:31 PM, John Rose via AGI <[email protected]> > wrote: >> Maybe we've been duped. Since bacteria have been around far longer than we >> have and since really we are hosts for them and we developed from single >> cell organisms perhaps... they essentially created us? And we've been >> designed to think that we are more intelligent for example how we thought >> that the universe revolved around the earth and how we are the only >> intelligent species, etc.. And when we die they eat us thus >> reverse-subsuming that temporal superorganismic intelligence probe back >> into their distributed knowledge hive. Essentially we're low entropy >> injections into the environment from their uber organismic spread of >> unicellular complexodynamical cogni-jelly. >> >> The more we learn the more we realize our insignificance and how godlike >> they are thus reaching a new level of self-awareness that the unicellulars >> are truly the first AGI designers and that general intelligence is >> actually just a dog and pony show for their bacteriological >> omni-intelligence. >> >> John >> >>> -----Original Message----- >>> From: Jim Bromer via AGI [mailto:[email protected]] >>> Sent: Thursday, February 12, 2015 9:31 PM >>> To: AGI >>> Cc: [email protected] >>> Subject: Re: [agi] A Polynomial Time Solution to 3-SAT >>> >>> How about bacteria programming COBOL using my no-distinction-between- >>> operand-and-operation computer language? >>> >>> Jim Bromer >>> >>> >>> On Thu, Feb 12, 2015 at 6:47 PM, Mike Archbold <[email protected]> >>> wrote: >>> > computing with salmonella and e coli bacteria? >>> > >>> > And some of you ridicule COBOL! >>> > >>> > On 2/12/15, Jim Bromer via AGI <[email protected]> wrote: >>> >> Microbes have reproduction constraints (complicated by food and waste >>> >> constraints) and the idea that a colony of bacteria could work on >>> >> successively more complicated graphs without running into >>> >> surface/reproduction constraints is a little hard to believe. Even >>> >> within a near future sci-fi system which includes modern micro >>> >> plumbing and micro cafeterias and other stuff that would allow the >>> >> system to work on more and more complicated problems the petri dish >>> >> could not solve the problem. If the Hamilton Problem could be solved >>> >> by breaking it into smaller parts it would not be (or no longer be) a >>> >> np-complete problem would it?. So the number of microbes that could >>> >> line the paths would be severely constrained. >>> >> Jim Bromer >>> >> >>> >> >>> >> On Thu, Feb 12, 2015 at 4:51 PM, Jim Bromer <[email protected]> >>> wrote: >>> >>>> Don't underestimate the complexity of chemical computation >>> >>>> occurring with microorganisms such as bacteria. The more it's >>> >>>> investigated the more underestimated the molecular sophistication >>> seems... >>> >>>> >>> >>>> Also FYI it's shown that NP-complete problems can be solved with >>> >>>> bacterial computers: >>> >>>> http://www.jbioleng.org/content/3/1/11/abstract >>> >>>> >>> >>>> John >>> >>> >>> >>> Do you understand the basics of their claims? How was the desired >>> >>> result represented? I mean I read the part about fluorescing both >>> >>> red and green, but does that mean that the two colonies were on >>> >>> either end of a 3-node directed path? It doesn't quite make sense >>> >>> to say that the bacterial computer can solve exponentially complex >>> >>> problems does it? Is a 3-node directed graph really evidence of an >>> >>> exponential to polynomial time solution, or is this really just an >>> >>> initial feasibility test? >>> >>> Jim Bromer >>> >>> >>> >>> >>> >>> On Thu, Feb 12, 2015 at 3:21 PM, John Rose via AGI <[email protected]> >>> >>> wrote: >>> >>>>> -----Original Message----- >>> >>>>> From: Matt Mahoney via AGI [mailto:[email protected]] >>> >>>>> >>> >>>>> 10^40 self replicating organisms over the last 3 billion years >>> >>>>> have long since solved the problem of traveling over snow without >>> >>>>> leaving footprints, but have failed to solve any NP-complete >>> >>>>> problems. >>> >>>>> >>> >>>> >>> >>>> Don't underestimate the complexity of chemical computation >>> >>>> occurring with microorganisms such as bacteria. The more it's >>> >>>> investigated the more underestimated the molecular sophistication >>> seems... >>> >>>> >>> >>>> Also FYI it's shown that NP-complete problems can be solved with >>> >>>> bacterial computers: >>> >>>> http://www.jbioleng.org/content/3/1/11/abstract >>> >>>> >>> >>>> John >>> >>>> >>> >>>> >>> >>>> >>> >>>> >>> >>>> ------------------------------------------- >>> >>>> AGI >>> >>>> Archives: https://www.listbox.com/member/archive/303/=now >>> >>>> RSS Feed: >>> >>>> https://www.listbox.com/member/archive/rss/303/24379807- >>> 653794b5 >>> >>>> Modify Your Subscription: https://www.listbox.com/member/?&; >>> Powered >>> >>>> by Listbox: http://www.listbox.com >>> >> >>> >> >>> >> ------------------------------------------- >>> >> AGI >>> >> Archives: https://www.listbox.com/member/archive/303/=now >>> >> RSS Feed: >>> >> https://www.listbox.com/member/archive/rss/303/11943661-d9279dae >>> >> Modify Your Subscription: >>> >> https://www.listbox.com/member/?&; >>> >> Powered by Listbox: http://www.listbox.com >>> >> >>> >>> >>> ------------------------------------------- >>> AGI >>> Archives: https://www.listbox.com/member/archive/303/=now >>> RSS Feed: https://www.listbox.com/member/archive/rss/303/248029- >>> 82d9122f >>> Modify Your Subscription: >>> https://www.listbox.com/member/?&; >>> 35e0de32 >>> Powered by Listbox: http://www.listbox.com >> >> >> >> >> ------------------------------------------- >> AGI >> Archives: https://www.listbox.com/member/archive/303/=now >> RSS Feed: https://www.listbox.com/member/archive/rss/303/3701026-786a0853 >> Modify Your Subscription: https://www.listbox.com/member/?&; >> Powered by Listbox: http://www.listbox.com > > > > -- > -- Matt Mahoney, [email protected] > > > ------------------------------------------- > AGI > Archives: https://www.listbox.com/member/archive/303/=now > RSS Feed: https://www.listbox.com/member/archive/rss/303/11943661-d9279dae > Modify Your Subscription: > https://www.listbox.com/member/?&; > Powered by Listbox: http://www.listbox.com > ------------------------------------------- AGI Archives: https://www.listbox.com/member/archive/303/=now RSS Feed: https://www.listbox.com/member/archive/rss/303/21088071-f452e424 Modify Your Subscription: https://www.listbox.com/member/?member_id=21088071&id_secret=21088071-58d57657 Powered by Listbox: http://www.listbox.com
